The Struggle
by aceofqueens
Summary: We know what happened to Shepard at the end of Mass Effect 3. We know about his battle with indoctrination. But what would it have looked like from Shepard's point of view? This story is a re-telling of the Mass Effect 3 ending through Shepard's eyes. It will follow the normal story but will contain some extra embellishment and head-cannon on my part.


**Read First: Author's Notes**

**This is the story of the end of Mass Effect 3, told through Shepard's eyes. Obviously, there will be heavy spoilers. This also assumes that the reader is familiar with the ending in detail. I recommend you do not read this story if you haven't finished the game (because it is a really awesome game), or you do not understand the ending. **

**To elaborate, I will be using something that was incorrectly dubbed "The Indoctrination Theory" (or IT) by some fans of the game that were dissatisfied with the way Mass Effect 3 ended. I will not be explaining the "theory", so if you do not know what it is, you must look elsewhere. There many great videos online that will do an excellent job of explaining it.**

**That said, Bioware did an excellent job. This work is not meant to contradict the ending at all. It is meant to put the focus on Commander Shepard and his thoughts, whereas the game focused on the player themselves. It's mostly cannon, but with my personal flair put onto it. Enjoy.**

Commander Shepard felt weak. His numerous wounds and the pang of sadness at Anderson's death sapped what little remained of his reserves of energy. He felt the life draining out of him as he sat next to the admiral's lifeless form. In all his life, the commander never recalled being this close to death.

_Well, except for the final moments before my first death, the one that ended in the void over Alchera, _he thought to himself.

This elicited a morbid smile from Anthony Shepard. He had few regrets, and he supposed that the prospect of a second death wasn't so bad. He had a few, though, such as the fact that he was forced to shoot Ashley Williams to death during the coup. There was also the fact that he was unable to save Mordin, Thane, or Legion.

_What did Garrus tell me? _He searched through his memory for the answer, unable to find it for a moment. _Ah yes, he said that humans just want to save everyone, but that it isn't possible. _

His turian friend's observation was correct, however. Shepard was overcome with relief when all twelve of his squad mates had survived the collector suicide mission. He had thought it was a miracle.

_If only it could have been that way one last time. If only this damn war hadn't required so many sacrifices. _

But the one sacrifice he regretted most was his own. Shepard did not fear death. After all, he had already died once before, and was dead long before he was born. Yet, the experience had not bothered him at all. He recalled a quote by an ancient writer called "Mark Twain" that said something similar. It had always been one of his favorites. What's more, as an atheist, Shepard did not fear the possibility of eternal damnation awaiting him. As far as he was concerned, death would be peaceful. And peace was something he felt he deserved—and had earned.

So it was not out of selfishness that he regretted his sacrifice, it born of the fact that those who knew him and still lived would suffer worse than he. Particularly, a certain quarian named Tali Zorah vas Normandy. He wished he could have lived, for her sake, and not for his. He feared not death, but leaving Tali to grieve. She had lost him once, so it felt like a betrayal to condemn her to the same fate once more. This thought filled him with pure sadness, but he refused to let tears fall.

Suddenly, a voice could be heard in Shepard's earpiece. It was Admiral Hacket, telling him that the Crucible hadn't fired.

_Strange, _he thought. _How is my ear piece functioning if my suit has no power? What is more concerning, how does Hacket know I'm here, specifically? Any one of those charging soldiers could have made it to the beam. My suit is offline, and my omni-tool is broken, so he shouldn't be able to pick up my life signs. _

Shepard pulled himself out of his thoughts and attempted to gather his energy so that he could move closer to the control panel. When he thought he had gathered enough strength, he attempted to stand. However, the critically-wounded commander flopped meekly down to the floor almost immediately.

"I…can't…" Shepard whispered before all he knew was blackness.

(…)

Shepard shook his head in confusion, trying to organize his thoughts. It was a lot of information to take in. After being lifted up by a beam of light, the "Star Child" (as he thought of it) had just given him a long lecture about the Reapers. His choices had been laid out to him, but Shepard still did not understand.

The Star Child had given him three options. The first was on his far left, where a blue light could be seen. This choice would supposedly allow Shepard to control the Reapers.

Commander Shepard was skeptical of this choice.

There were so many problems with it. The most obvious was that there was no guarantee that Shepard would still have free will in the new form that the Star Child said he would take. What if he was just made into an exact copy of the Star Child? In that case, the "new Shepard", so to speak, might not want to stop the Reapers at all.

Secondly, Shepard knew that the idea that the Reapers could and should be controlled was always held by those who were indoctrinated. _If I start thinking that way, I'll become indoctrinated. Just like the Illusive Man. _Shepard was not about to let himself fall onto the Reaper's side after he had just argued with the Illusive Man for doing exactly that.

Control was not an option. Shepard refused to consider it.

He turned his head right to look down the center walkway. There was another option. Synthesis, as the Star Child had called it. It was a choice that would "merge synthetic and organic life." While on the surface it sounded like a good compromise between the other two options, Shepard instantly saw many problems with it.

First, what would the device do, specifically? After all, "merge synthetic and organic life" was a very vague explanation. Would it kill all currently living synthetics and organics, using their bodies and DNA to make new life forms that were both organic and synthetic? That sounded correct, as the Star Child had stated it would make "new life." Or perhaps it would simply give organics some cybernetics or something. The machine's use was far too unclear for Shepard.

And if that wasn't enough, whatever it did, there was no reason to think that whatever "new life" was created would be better than the old life. Shepard rather liked the current species of the galaxy, excluding the batarians who tried to enslave and kill everyone else whenever they had a chance.

Thirdly, even if the synthesis improved all life, Shepard knew he would still be killing those trillions of people he had been trying to save the whole time. It would be essentially throwing away the hard work of three long years. It would be throwing away all the noble sacrifices made by men, women, and asari across the galaxy. And if synthesis didn't kill everyone, well then that would be even worse! Rewriting the DNA of everyone in the galaxy and irreversibly changing them without permission would be the most immoral thing he could think of.

Shepard recalled a time when he helped Shiala free the people of Zhu's Hope from a contract which allowed Baria Frontiers to experiment on them without consent. What synthesis was proposing was hundreds of times worse than what Baria Frontiers intended to do to those poor Zhu's Hope colonists. Shepard would not stand for it.

Fourth, he realized that synthesis was the option that Saren Arterius would have selected. He vividly remembered his many talks with the Turian ex-spectre, word-for-word. Saren definitely wanted to merge organic and synthetic life, to be one with the reapers. He also remembered convincing Saren to kill himself because he was indoctrinated. Why was he indoctrinated? Because his goal was the very thing that synthesis proposed. Shepard knew with absolute certainty that if he chose synthesis; he would be indoctrinated just as his old enemy was.

And lastly, if the Star Child, who claimed to be the Reapers' collective mind, knew so much about synthesis, why had the Reapers not simply built and used the device many millennia ago? It would achieve their ultimate goal: the merging of organics and synthetics. The Star Child even called it "the pinnacle of evolution", which was a topic that the Reapers seemed obsessed with.

_I can't choose synthesis. _He told himself.

Shepard moved his head once more, so that he could gaze upon the last option. Destroy. The Star Child had told him that this would kill all synthetic life in the galaxy, ending the Reapers, the Geth, and himself. It certainly seemed like a good choice. The Reapers would be forever eliminated, never to return. This would be over once and for all, at the cost of only himself, EDI, and the Geth. But several things gave him pause.

_The Star Child said that this option would destroy me. _He thought. _But I'm not a synthetic. Just because I have cybernetics doesn't mean I count as a synthetic. Most of my body is organic. And besides, you need to be an AI to be considered synthetic life. _

Another detail bothered him as well. _What about the Geth? How can a device that destroys Reapers also destroy synthetic life such as the Geth anyway? The Reapers are no more synthetic than I am, because they're equally organic as anything else. How could the Crucible possibly kill the sentient starships if it targeted synthetics?_

The answer was simple. The Crucible couldn't possibly destroy synthetic life. If it was designed to kill Reapers, the only way would be to make it target Reaper technology specifically. So why had the Star Child lied to him? It was almost as if…

Shepard whipped his head around to look at the child in question. At that moment, there was suddenly a wonderful explosion of realization inside his mind. Shepard had an epiphany and everything crystallized. It all made sense.

He knew there was something familiar about the Star Child the moment he saw it. But now Shepard knew why. The Star Child was the same kid he had seen outside the evac shuttle on earth just as the Normandy was lifting off. The same kid who had inexplicably climbed a wall, stared at a Reaper, survived a Reaper's lazer beam, instantly disappeared when Shepard looked away, and to top it all off, had somehow made it to the evac shuttle. And this Star Child looked EXACTLY the same.

Shepard knew of two possibilities. One: the Reapers had access to his mind and were making the kid from earth appear as an illusion. Or two: The Reapers had planted the kid in his mind all along, and were using the same trick again now.

The second option seemed highly likely to Shepard, since it would explain the strange dreams he had been having that featured the very same kid. Either way, however, there was one thing that was certain: the Reapers were trying to indoctrinate him. Most likely it was a last ditch effort to stop him from activating the Crucible.

That was why the Star Child had tried to make destroy seem like a bad option and push him toward one of the options that would indoctrinate him. Shepard would have had to be an idiot to not understand that the Reapers couldn't indoctrinate him through force of will. They needed someone to indoctrinate themselves. They could nudge someone over to their side, sure, but not completely. This was knowledge Shepard had learned from paying basic attention to the things that had happened to him so far.

Destroy was the way out of this nightmare (for it most certainly was a dream, or some sort of illusion at least). Shepard grinned wickedly, the same triumphant grin that he wore when the Quarians and Geth had made peace, when he watched the Collector homeworld explode, and when he had stood victorious on top of the pieces of Sovereign's body. Only this time, it was a smile that contained the pride of a man who had resisted something that no victim of the Reapers had resisted before.

He limped forward, taking the walkway that led to the right. A foul scream reached his ears.

"No! Think about what you're doing Shepard!" It was the screech of the Star Child, who stood far away. "Synthetics will return, and chaos will come back. There will be war between organics and synthetics."

Shepard turned around to face the illusion. "You and I both know there will be no war. You lied to me, Harbinger, and it was a pitiful attempt to deceive a foe that, using your own words, is 'infinitely your greater'. I've seen right through your illusion. The Reapers have lost."

"Shepard you…" the Star child began to say with Harbinger's voice, before it was interrupted by the Commander.

"You don't even get the last word, you pathetic insect. Get out of my galaxy."

And with that, Shepard fired his carnifex into the Star Child's head. It was a perfect shot, right between the eyes from a considerable distance away.

Shepard's defiance dispelled the illusion, and the Star Child disappeared without a word. Shepard then turned around without a second thought and walked toward the power conduit with increased energy.

He fired round after round into the conduit, shattering its glass. The fact the heavy pistol never needed thermal clips to be exchanged added further proof that Shepard was right.

There was a blast of cleansing fire, and everything went black once more.

(...)

He expected to awaken on earth's soil near the beam. Instead, he found himself on a cold metal floor. Shepard slowly pushed himself upright and looked around.

He was in the control room of the Citadel, standing a few feet away from the main console. Hacket was speaking to him through his earpiece.

"Shepard! Commander, please tell me you can hear me."

The Commander was surprised at this fact. He looked down and saw his unscathed and fully functional armor. The Illusive Man and Anderson's corpses were nowhere to be seen.

_It had been a hallucination all along._ He told himself. There were dozens upon dozens of things that had happened before he passed out that Shepard now realized were utterly nonsensical and dream- like. They seemed so obvious now, but had been muddy and blurred in the half-hallucination brought on by indoctrination that he had failed to notice them.

_Like the headaches and inky darkness. I of all people should have realized the signs of indoctrination. And Anderson's gunshot wound magically moving to my body? How could I have missed that?_

"Hello Admiral, this is Shepard."

"Good god man, you're alive? We're being torn apart out here. You need to get to that control console now."

"I'm on it sir, I just had a little…snafu." Shepard explained. He stepped forward and pressed a few holographic buttons. "It's done, Admiral."

Admiral Hacket was silent, as was Shepard. It was the tensest moment of the first human spectre's life.

The moment was ended by a thunderous boom. The control room shook and Shepard struggled for his balance.

"The Crucible is firing, Shepard. We've done it!" Hacket was exclaiming victoriously over the communications channel. "You had better get out of there. I think there may be an-"

A blast of superheated flame filled the room before Hacket finished the sentence. Shepard felt a surge of adrenaline and channeled his reflexes, just the way he had done countless times in combat. He quickly scooped up his helmet and placed it over his head. Not a moment later, the blast propelled Commander Shepard out of the Citadel Tower and into the void.

_At least my suit isn't leaking air this time _he thought to himself. _And my shields seem to have absorbed the heat. _

Shepard continued to move through space, the force of the blast small enough to prevent him from spinning around and around, but still large enough to keep him moving. He glanced down and could tell he was in the middle of the Citadel, passing over a glowing arm below.

After realizing this, he twisted around so he could see the results of the Crucible. A red point of light seemed to be gathering at the end of the massive device. Before this could be pondered, the energy seemed to release itself with an explosion, followed by a wave of static electricity, which was also red.

The Commander had the privilege of watching the mighty blast cascade over the Reapers, leaving them crackling with electricity and turned upside down like dead insects.

_So it did work, after all. They're beaten, finally beaten. I…no…we have done it. _He wanted to share this victory with someone, but was instead floating alone in space.

It was then that he also noticed that the red wave tearing pieces of the Citadel apart and shutting off some of the lights. That meant most of it wouldn't have gravity or an atmosphere any longer. He needed someone to come pick him up, as help from the Citadel seemed unlikely. He tried to hail the Normandy.

"Come in, Joker. This is Shepard. I'm floating in the middle of the Citadel and need evac," he said with his gloved hand pressing a button on the exterior of his helmet. There was no response, save for a small amount of white noise. It was surely broken by the explosion.

Normally if he was on a mission the spectre would have ducked behind some cover and repaired his comm. system himself, but he needed to remove his helmet to do so. And in the vacuum of space, he simply could not do that.

_Damn. _He angrily thought. _There goes my chance of a rescue. I wonder if…_

But the Commander stopped his thought when he saw a faint light approaching from out of the corner of his eye. It grew larger and larger over several minutes.

_It's a shuttle! But Steve's was shot down on Earth. This must be from the Citadel. How did they know I was here?_

The shuttle pulled up next to the Commander, the doors opening with a hiss. Instantly the interior depressurized, letting out the atmosphere within. Crates, piles of weapons, and thermal clips were sucked out as well.

The craft was a few dozen yards from his right, so whoever was piloting it banked left. Shepard passed through the open door and slammed into the far wall, jarring his shoulder. The maneuver was clumsy, meaning the pilot was likely an amateur.

The doors closed a moment later, sealing Sheppard inside. Immediately the craft took off, heading straight for one of the parts of the Citadel that still had power.

Shepard was curious as to the identity of his rescuer, so he sat down in the co-pilot's chair of the cockpit and took a look.

It was clearly a male human, but more than that the spectre could not say. He wore blue camouflaged alliance combat armor and his helmet obscured his face.

Whoever it was, the Commander knew he owed them a great debt. Unfortunately, he could not relay his thanks to this person, due to the broken communicator. He guessed this man would reveal himself once they landed on the Citadel and it was safe for him to remove his helmet. Then, he would make his gratitude known.

(…)

The Kodiak finally touched down on a damaged citadel street. The ride had been bumpy, but Shepard did not care. He was alive, and that was enough.

The mysterious pilot touched a holographic button and all doors on the Kodiak opened, letting air back inside. Shepard quickly removed his helmet so he could speak.

The rescuer followed suit, revealing his face. When Shepard saw it, he was absolutely shocked.

It was none other than Conrad Verner.

"Commander, it's me! Conrad Verner. I'm the one who rescued you."

"Conrad, I've never been happier to see you in my life. How did you know I was up there?"

"Well, to be honest, I wasn't sure." The blond Shepard-fan answered with an excited tone. "It was more of a hunch. When I saw the arms of the Citadel opening, I knew only the great commander Shepard could have done it. But then there was a huge explosion from the Citadel Tower, and I knew what I to do. I had to get up there to rescue you, but the ship's scanners found you floating around instead."

"Conrad, how did you get this ship and armor?" Shepard asked with a skeptical look on his face.

"The Keepers, see, they were locking down the whole place. Much before you opened the arms." Conrad was talking a mile a minute by now. "Anyone who tried to hack through doors or bypass security got shot by mechs. I took this armor and some guns from a dead alliance soldier so I could protect people and be a hero like you. I know you told me not to try to be like you anymore, but I just had to. When I saw that big machine docking on the Citadel and the explosion right after, I stole this shuttle to come get you."

Shepard smiled and shook his head. He couldn't believe what he was hearing. "You're a good man, Conrad, and I'm glad you did what you did. You saved my life today." Shepard then leaned forward and shook Conrad's hand firmly.

(…)

Soon after, Shepard repaired his comm. system and contacted both Hacket and the Normandy. Everyone had been ecstatic to learn that Shepard was alive. Especially Tali, who had locked herself in the Commander's quarters because she thought him dead.

As Shepard was waiting on the Citadel for pickup by the Normandy, he pondered everything that had happened that day. The Reapers were defeated, the war over.

However, the road to recovery would be a long one indeed. The Citadel and Mass Relays would need repairing. Earth, Palaven, Sur'Kesh, and Thessia would need to be rebuilt (some more than others); but Commander Shepard was sure that those tasks could be accomplished. The Galaxy would still have need of him, sure, but he was content that the hard part was over.

**(A/N: I hope you enjoyed it. I decided to put a personal touch on exactly how Commander Shepard survives, since it's ambiguous in the game. Conrad was one of my favorite characters and I thought it would have been awesome for him to be the one that rescues Shepard in the end. Provided he lives, of course, which he did in my playthrough. **

**Anyways, please review. I'd like to know if I'm doing anything right or wrong. If people seem to like my writing, I may do a post-ME3 fic about what I think would be in store for Shepard and the Galaxy after the Reaper war. I have lots of ideas!)**


End file.
